I try to avoid knee-jerk Microsoft bashing, but they're really making it hard.
Sounds like compatibility is fine? Honestly, I'm okay with the 360 pad support taking over--Almost every controller had a standard button layout, but with the buttons oddly numbered from controller to controller. Newer controllers all mapping to 360 buttons has simplified everything.
It's sad that my original Logitech DualAction isn't quite as useful, but the newer models have had so many fewer issues when it comes to just using them in a game.
It was indeed annoying that the pad manufacturers couldn't get their shit together and agree on a button ordering, but that doesn't excuse Microsoft inventing an entirely new and unnecessary standard instead of just declaring their own canonical ordering.
There's an established standard for USB gamepads, and Microsoft (a) ignored it in favor of their own proprietary standard Xinput and (b) convinced quite a lot of devs to only support Xinput. This means that a perfectly functional Logitech or Saitek gamepad from the late 2000s is useless with modern games, and a 360 pad is useless with older games, unless you jump through hoops with drivers. It also means that it's difficult to get a 360 pad working correctly on non-Windows platforms.
It makes no sense that the Xbone controller, which has the same controls in the same places as the 360 controller, wasn't backwards-compatible out of the box; and I'm suspicious that they'll push devs to support the Xbone pad exclusively to force 360-pad owners to upgrade, because they've already done that once.
"Am I missing something, or did they just break backwards compatibility again?"
And... no, they didn't, the Xbox One controller (per the linked article) is backwards compatible with PC games who use the 360 controller. So you ARE missing something, something you could have discovered easily by reading the article you're commenting on.
So... you were clear, you were just wrong.
http://msdn.microsoft.com/en-us/library/windows/desktop/ee41...
(Their explanation is "the Xbox 360 controller was designed to register minimum value, not center, when the triggers are not being held." Seems like the obvious solution would be "don't do that.")